How are the repeats determined?

Repeats are determined in several ways.

• 1) [RepeatMasker]
  

There are RepeatMasker libraries available for C.elegans andC.briggsae are available from the [Sanger Institute pages].  These pages also have some description of the motifs identified.  They can be found in the GFF files thus . .

CHROMOSOME_III  RepeatMasker    repeat_region   9559    9734    837     .       .       Target "Motif:PALTA5_CE" 126 307

• 2) [Tandem Repeat Finder.] by G. Benson

These can be found in the GFF files thus . .

CHROMOSOME_III  tandem  tandem_repeat   5079    5117    55      .       .       Note "3 copies of 14mer"

• 3) [dust]a low-complexity filter for nucleotide sequences (available from WS193)
  
• 4) inv  - inverted repeat finding tool by R. Durbin (unpublished)

CHROMOSOME_III  inverted        inverted_repeat 9482    9734    69      .       .       Note "loop 877, 3 gaps"